chr1-163444769-C-T

Variant names:

• chr1-163444769-C-T
• rs4265409
• ENST00000759058.1:n.148+4288C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000759058.1(ENSG00000298925):​n.148+4288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,054 control chromosomes in the GnomAD database, including 15,593 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (15593 hom., cov: 32)
• Consequence: ENSG00000298925 ENST00000759058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 15 publications found

Genes affected

ENSG00000298925 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759058.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298925	ENST00000759058.1		n.148+4288C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64305 AN: 151934 Hom.: 15576 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.464

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.423 AC: 64366 AN: 152054 Hom.: 15593 Cov.: 32 AF XY: 0.439 AC XY: 32654 AN XY: 74312

African (AFR) AF: 0.222 AC: 9227 AN: 41476

American (AMR) AF: 0.549 AC: 8383 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4986 AN: 5170

South Asian (SAS) AF: 0.722 AC: 3476 AN: 4812

European-Finnish (FIN) AF: 0.481 AC: 5077 AN: 10558

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29979 AN: 67972

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.452 Hom.: 35418

Bravo AF: 0.416

Asia WGS AF: 0.789 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.077
DANN	Benign	0.27
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4265409; hg19: chr1-163414559;